Pharmaceutical products require appropriate quality control, which comprises a set of tests aimed at the determination of assays of the substances. Chromatographic methods are one of the most abundant analytical methods applied in routine analyses of pharmaceuticals. Information on the behavior of the compounds under certain analytical conditions is valuable in the process of analytical method development. This work was aimed at revealing the impact of substituents of various natures at two positions of triazole ring on the behavior of new 3-thio-1,2,4-triazoles under GC-MS conditions and evaluating the applicability of GC-MS method for the analysis of these compounds. Gas chromatography was used in combination with mass spectrometry. New 1,2,4-triazole derivatives were obtained at the Department of Natural Sciences for International Students and Toxicological Chemistry of Zaporizhzhia State Medical University. For the experiment, two groups of compounds were formed, each having different substituents at C-3 and C-5 of triazole molecule, respectively. The analysis was held using Agilent 7890B GC system coupled with Agilent 5977B mass selective detector. Compounds were separated on a non-polar column. The following parameters were assessed and compared for identification and study of chromatographic behavior of the compounds: mass spectra, retention times, symmetry factors, and relative responses (against reference compound). It was shown that there is no direct relation between melting point and retention time; instead, the nature of substituents significantly affects the chromatographic behavior. The strongest response belongs to compounds that have phenyl moiety at C-5 and alkyl substituent attached through thiol group at C-3 of the triazole ring. Thiophen-2-yl and methyl at C-5, as well as acetate and ester groups attached through thiol group at C-3 of the cycle, decrease chromatographic response. GC-MS can be applied for the analysis of biologically active 1,2,4-triazoles, though with several limitations. The higher the polarity of the compound, the worse the response and peak shape; these circumstances complicate GC-MS analysis of 1,2,4-triazole derivatives. Apart from providing information on physicochemical properties of the compounds, the obtained experimental data provide some valuable insights into permeability of the new triazole derivatives through biological membranes, which could be useful in drug design.